wip/nanoplot: import nanoplot version 1.38.0.20210602 as wip/nanoplot

[Brook Milligan <brook%nmsu.edu@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Brook Milligan <brook%nmsu.edu@localhost>
Pushed By:	brook
Date:		Tue Jun 8 06:59:18 2021 -0600
Changeset:	61ee8eed2d367eb7a01f0213b0a4dabcf87466f6

Modified Files:
	Makefile
Added Files:
	nanoplot/DESCR
	nanoplot/Makefile
	nanoplot/PLIST
	nanoplot/distinfo

Log Message:
wip/nanoplot: import nanoplot version 1.38.0.20210602 as wip/nanoplot

Plotting tool for long read sequencing data and alignments.

This script performs data extraction from Oxford Nanopore sequencing
data in the following formats:

- fastq files (can be bgzip, bzip2 or gzip compressed)

- fastq files generated by albacore, guppy or MinKNOW containing
  additional information (can be bgzip, bzip2 or gzip compressed)

- sorted bam files

- sequencing_summary.txt output table generated by albacore, guppy or
  MinKnow basecalling (can be gzip, bz2, zip and xz compressed)

- fasta files (can be bgzip, bzip2 or gzip compressed)

Multiple files of the same type can be offered simultaneously

NanoPlot creates:
- a statistical summary
- a number of plots
- a html summary file

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=61ee8eed2d367eb7a01f0213b0a4dabcf87466f6

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 Makefile          |  1 +
 nanoplot/DESCR    | 23 +++++++++++++++++++++++
 nanoplot/Makefile | 43 +++++++++++++++++++++++++++++++++++++++++++
 nanoplot/PLIST    | 42 ++++++++++++++++++++++++++++++++++++++++++
 nanoplot/distinfo |  6 ++++++
 5 files changed, 115 insertions(+)

diffs:
diff --git a/Makefile b/Makefile
index 1d4186ac6a..3551167cca 100644
--- a/Makefile
+++ b/Makefile
@@ -2468,6 +2468,7 @@ SUBDIR+=	nanofilt
 SUBDIR+=	nanoget
 SUBDIR+=	nanolyse
 SUBDIR+=	nanomath
+SUBDIR+=	nanoplot
 SUBDIR+=	nanostat
 SUBDIR+=	naqsh-ttf
 SUBDIR+=	nary
diff --git a/nanoplot/DESCR b/nanoplot/DESCR
new file mode 100644
index 0000000000..b3363c479b
--- /dev/null
+++ b/nanoplot/DESCR
@@ -0,0 +1,23 @@
+Plotting tool for long read sequencing data and alignments.
+
+This script performs data extraction from Oxford Nanopore sequencing
+data in the following formats:
+
+- fastq files (can be bgzip, bzip2 or gzip compressed)
+
+- fastq files generated by albacore, guppy or MinKNOW containing
+  additional information (can be bgzip, bzip2 or gzip compressed)
+
+- sorted bam files
+
+- sequencing_summary.txt output table generated by albacore, guppy or
+  MinKnow basecalling (can be gzip, bz2, zip and xz compressed)
+
+- fasta files (can be bgzip, bzip2 or gzip compressed)
+
+Multiple files of the same type can be offered simultaneously
+
+NanoPlot creates:
+- a statistical summary
+- a number of plots
+- a html summary file
diff --git a/nanoplot/Makefile b/nanoplot/Makefile
new file mode 100644
index 0000000000..9f956ba171
--- /dev/null
+++ b/nanoplot/Makefile
@@ -0,0 +1,43 @@
+# $NetBSD$
+
+GITHUB_PROJECT=	NanoPlot
+GITHUB_TAG=	aa8b718
+DISTNAME=	NanoPlot-1.38.0.20210602
+CATEGORIES=	biology python
+MASTER_SITES=	${MASTER_SITE_GITHUB:=wdecoster/}
+DIST_SUBDIR=	${GITHUB_PROJECT:tl}
+
+MAINTAINER=	pkgsrc-users%NetBSD.org@localhost
+HOMEPAGE=	https://github.com/wdecoster/NanoPlot
+COMMENT=	Plotting suite for Oxford Nanopore sequencing data and alignments
+LICENSE=	gnu-gpl-v3
+
+DEPENDS+=	${PYPKGPREFIX}-biopython>=1.74:../../biology/py-biopython
+DEPENDS+=	# TODO: pysam>0.10.0.0
+DEPENDS+=	${PYPKGPREFIX}-pandas>=0.22.0:../../math/py-pandas
+DEPENDS+=	${PYPKGPREFIX}-scipy>=1.6.3:../../math/py-scipy
+DEPENDS+=	# TODO: python-dateutil>=0
+DEPENDS+=	${PYPKGPREFIX}-seaborn>=0.9.0:../../graphics/py-seaborn
+DEPENDS+=	${PYPKGPREFIX}-matplotlib>=3.1.3:../../graphics/py-matplotlib
+DEPENDS+=	nanoget>=1.12.0:../../wip/nanoget
+DEPENDS+=	nanomath>=1.0.0:../../wip/nanomath
+DEPENDS+=	# TODO: pauvre==0.2.0>=0
+DEPENDS+=	# TODO: plotly>=4.1.0
+DEPENDS+=	# TODO: pyarrow>=0
+DEPENDS+=	# TODO: kaleido>=0
+DEPENDS+=	${PYPKGPREFIX}-scikit-learn>=0.22.1:../../math/py-scikit-learn
+DEPENDS+=	${PYPKGPREFIX}-joblib>=1.0.1:../../devel/py-joblib
+
+WRKSRC=		${WRKDIR}/NanoPlot-aa8b71872d4204f7aad4d6da8f87107e7fb4c748
+USE_LANGUAGES=	# none
+
+EGG_NAME=	${DISTNAME:C/\.[[:digit:]]+$$//}
+
+post-install:
+	${RM} ${DESTDIR}${PREFIX}/LICENSE
+	${RM} -r ${DESTDIR}${PREFIX}/${PYSITELIB}/scripts
+
+BUILDLINK_API_DEPENDS.py-numpy+=	${PYPKGPREFIX}-numpy>=1.20.3
+.include "../../math/py-numpy/buildlink3.mk"
+.include "../../lang/python/egg.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/nanoplot/PLIST b/nanoplot/PLIST
new file mode 100644
index 0000000000..311911e06d
--- /dev/null
+++ b/nanoplot/PLIST
@@ -0,0 +1,42 @@
+@comment $NetBSD$
+bin/NanoPlot
+${PYSITELIB}/${EGG_INFODIR}/PKG-INFO
+${PYSITELIB}/${EGG_INFODIR}/SOURCES.txt
+${PYSITELIB}/${EGG_INFODIR}/dependency_links.txt
+${PYSITELIB}/${EGG_INFODIR}/entry_points.txt
+${PYSITELIB}/${EGG_INFODIR}/requires.txt
+${PYSITELIB}/${EGG_INFODIR}/top_level.txt
+${PYSITELIB}/extra/color_options_hex.txt
+${PYSITELIB}/nanoplot/NanoPlot.py
+${PYSITELIB}/nanoplot/NanoPlot.pyc
+${PYSITELIB}/nanoplot/NanoPlot.pyo
+${PYSITELIB}/nanoplot/__init__.py
+${PYSITELIB}/nanoplot/__init__.pyc
+${PYSITELIB}/nanoplot/__init__.pyo
+${PYSITELIB}/nanoplot/filteroptions.py
+${PYSITELIB}/nanoplot/filteroptions.pyc
+${PYSITELIB}/nanoplot/filteroptions.pyo
+${PYSITELIB}/nanoplot/report.py
+${PYSITELIB}/nanoplot/report.pyc
+${PYSITELIB}/nanoplot/report.pyo
+${PYSITELIB}/nanoplot/utils.py
+${PYSITELIB}/nanoplot/utils.pyc
+${PYSITELIB}/nanoplot/utils.pyo
+${PYSITELIB}/nanoplot/version.py
+${PYSITELIB}/nanoplot/version.pyc
+${PYSITELIB}/nanoplot/version.pyo
+${PYSITELIB}/nanoplotter/__init__.py
+${PYSITELIB}/nanoplotter/__init__.pyc
+${PYSITELIB}/nanoplotter/__init__.pyo
+${PYSITELIB}/nanoplotter/nanoplotter_main.py
+${PYSITELIB}/nanoplotter/nanoplotter_main.pyc
+${PYSITELIB}/nanoplotter/nanoplotter_main.pyo
+${PYSITELIB}/nanoplotter/plot.py
+${PYSITELIB}/nanoplotter/plot.pyc
+${PYSITELIB}/nanoplotter/plot.pyo
+${PYSITELIB}/nanoplotter/spatial_heatmap.py
+${PYSITELIB}/nanoplotter/spatial_heatmap.pyc
+${PYSITELIB}/nanoplotter/spatial_heatmap.pyo
+${PYSITELIB}/nanoplotter/timeplots.py
+${PYSITELIB}/nanoplotter/timeplots.pyc
+${PYSITELIB}/nanoplotter/timeplots.pyo
diff --git a/nanoplot/distinfo b/nanoplot/distinfo
new file mode 100644
index 0000000000..d27eb80438
--- /dev/null
+++ b/nanoplot/distinfo
@@ -0,0 +1,6 @@
+$NetBSD$
+
+SHA1 (nanoplot/NanoPlot-1.38.0.20210602-aa8b718.tar.gz) = c857c123b96c54ea538008740641d6e7db12f8af
+RMD160 (nanoplot/NanoPlot-1.38.0.20210602-aa8b718.tar.gz) = 57c4ddf6a4ecd4fafa7fc3bff132bf7fc6533036
+SHA512 (nanoplot/NanoPlot-1.38.0.20210602-aa8b718.tar.gz) = d2fb58e1c965d7ed425c863a78c4164fb7c78d990363eba9559177ad6e672b6663de6169b2d6409d7e4fe9298830c8a3cb3b325898ee3f3e033dc6a110ba598d
+Size (nanoplot/NanoPlot-1.38.0.20210602-aa8b718.tar.gz) = 843854 bytes